How can I remove objects via datablocks outliner?
[Edit 2 Jan, 2016] You can delete datablocks of any type by way of the outliner window. Find the object, select it in the outliner, right-click on the item, and select "delete" from the context menu.

[Original answer]

But you wrote in your question that many of your files are 


  "suffering from 2 empties". 


Your problem might be that these can't be deleted as empties, because they are phantom bones and not empties at all. You will probably find the objects you want to delete if you look under the armatures in your file. You don't need to be in datablock view to do this. If you select the armatures in the "all scenes" view of the outliner one by one, I expect you will find which armature contains the bones (or that the two bones may not be in the same armature. In either case, in object mode in the 3D viewport, looking under armatures, I expect you will be able to delete the phantom bones.

But, it might want to be careful about deleting the bones, because it is possible to delete a bone from the middle of a chain, so that there may be other bones connected as children of the phantom bone which will be deleted if you delete the phantom bone.